When you've "been on" a website, it means that you've visited it. The word "visit" sounds a little to formal for friendly conversation, though. So in casual conversation, people ask:

Have you been on People.com recently?

One other note: you use "been on" for large websites with a lot of functionality, like Facebook, Twitter, eBay, etc. For smaller websites that don't do much (like PhraseMix.com), you should use "been to" instead.